Variant report

Variant	rs4662724
Chromosome Location	chr2:128137561-128137562
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:128135797..128138082-chr2:128165864..128167455,2	MCF-7	breast:
2	chr2:128131816..128133324-chr2:128137247..128139883,2	K562	blood:
3	chr2:128122312..128124087-chr2:128136943..128139577,2	MCF-7	breast:
4	chr2:128136753..128139977-chr2:128144092..128148521,5	K562	blood:
5	chr2:128134227..128136528-chr2:128137224..128139404,2	K562	blood:
6	chr2:128128959..128132166-chr2:128135753..128139154,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169967	Chromatin interaction
ENSG00000236682	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10167294	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10928764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1143407	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11684068	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11899601	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12613252	0.87[EUR][1000 genomes]
rs12613254	0.87[EUR][1000 genomes]
rs12613413	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12614320	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12617858	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12619391	0.87[EUR][1000 genomes]
rs13017103	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13034157	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13390029	0.87[EUR][1000 genomes]
rs13403918	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13409933	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13414676	0.87[EUR][1000 genomes]
rs13429925	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2134794	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2139142	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276682	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276683	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28807127	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3088374	0.91[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs34006114	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34487399	0.80[EUR][1000 genomes]
rs34601617	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34703177	0.95[CEU][hapmap];0.81[GIH][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs35708549	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3738948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3893313	0.82[EUR][1000 genomes]
rs4150434	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150492	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150514	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4300780	0.87[EUR][1000 genomes]
rs4359587	0.82[EUR][1000 genomes]
rs4662721	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58063879	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59027829	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6430937	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6716392	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6735779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6747862	0.95[CEU][hapmap]
rs6761391	0.80[CHB][hapmap];0.83[ASN][1000 genomes]
rs67771362	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7584659	0.84[ASN][1000 genomes]
rs9923	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs4662724	MAP3K2	cis	cerebellum	SCAN
rs4662724	GYPC	cis	parietal	SCAN
rs4662724	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs4662724	AC068282.3	cis	Artery Aorta	GTEx
rs4662724	AC068282.3	cis	Muscle Skeletal	GTEx
rs4662724	MAP3K2	cis	lymphoblastoid	seeQTL
rs4662724	AC068282.3	cis	Whole Blood	GTEx
rs4662724	AC068282.3	cis	lung	GTEx
rs4662724	AC068282.3	cis	Heart Left Ventricle	GTEx
rs4662724	AC068282.3	cis	Esophagus Muscularis	GTEx
rs4662724	AC068282.3	cis	Nerve Tibial	GTEx
rs4662724	MAP3K2	cis	Cerebellum	GTEx
rs4662724	AC068282.3	cis	Esophagus Mucosa	GTEx
rs4662724	MAP3K2	cis	multi-tissue	Pritchard
rs4662724	AC068282.3	cis	Stomach	GTEx
rs4662724	AC068282.3	cis	Thyroid	GTEx
rs4662724	MAP3K2	cis	Brain Pons	GTEx
rs4662724	TUBA3E	cis	parietal	SCAN
rs4662724	MAP3K2	cis	Frontal Cortex	GTEx
rs4662724	MAP3K2	cis	Temporal Cortex	GTEx
rs4662724	AC068282.3	cis	Skin Sun Exposed Lower leg	GTEx
rs4662724	AC068282.3	cis	Artery Tibial	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128107800-128140200	Weak transcription	Gastric	stomach
2	chr2:128120800-128139200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:128120800-128142000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:128122200-128142200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:128123400-128137600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:128123400-128140400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:128123400-128144200	Weak transcription	Colonic Mucosa	Colon
8	chr2:128124000-128140000	Weak transcription	Left Ventricle	heart
9	chr2:128128000-128144000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr2:128128000-128144000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:128128400-128142200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:128128600-128140000	Weak transcription	Aorta	Aorta
13	chr2:128129800-128140200	Weak transcription	Right Ventricle	heart
14	chr2:128131800-128139200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:128132400-128140800	Weak transcription	Fetal Lung	lung
16	chr2:128132800-128144000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:128133200-128142400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:128133800-128139200	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:128134200-128140200	Weak transcription	Ovary	ovary
20	chr2:128134200-128141400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:128134400-128140000	Weak transcription	Psoas Muscle	Psoas
22	chr2:128134400-128140200	Weak transcription	Lung	lung
23	chr2:128134400-128142200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:128134400-128144000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:128134600-128137600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr2:128134600-128137600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:128134600-128137600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:128134600-128138200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr2:128134600-128140600	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:128134600-128142000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr2:128134600-128142200	Weak transcription	Thymus	Thymus
32	chr2:128134600-128142800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:128134600-128143000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:128134600-128143200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr2:128134600-128143600	Weak transcription	Fetal Intestine Large	intestine
36	chr2:128134600-128143800	Weak transcription	Fetal Stomach	stomach
37	chr2:128134600-128143800	Weak transcription	Fetal Thymus	thymus
38	chr2:128134600-128144200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr2:128134600-128144400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:128134600-128144400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:128135400-128137800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:128135400-128139400	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr2:128135400-128141000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:128135400-128141200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr2:128135400-128141600	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr2:128135400-128144000	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:128135600-128137600	Weak transcription	Adipose Nuclei	Adipose
48	chr2:128135600-128142000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:128135600-128142000	Weak transcription	Small Intestine	intestine
50	chr2:128135600-128142200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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